1The W.M. Keck Center for Comparative and Functional Genomics
2Department of Animal Sciences
3Biophysics and Computational Biology Program
University of Illinois at Urbana-Champaign
Urbana, IL 61801
Received on November 9, 2003; accepted on November 11, 2003
ABSTRACT
Motivation:The completion of human and mouse genome
sequences provides a valuable resource for decoding other
mammalian genomes. The comparative mapping by annotation
and sequence similarity (COMPASS) strategy takes
advantage of the resource and has been used in several
genome-mapping projects. It uses existing comparative genome
maps based on conserved regions to predict map
locations of a sequence. An automated multiple-species
COMPASS tool can facilitate in the genome sequencing effort
and comparative genomics study of other mammalian species.
Results: The prerequisite of COMPASS is a comparative
map table between the reference genome and the predicting
genome. We have built and collected comparative maps
among five species including human, cattle, pig, mouse and
rat. Cattle-human and pig-human comparative maps were
built based on the positions of orthologous markers and the
conserved synteny groups between human and cattle and
human and pig genomes, respectively. Mouse-human and
rat-human comparative maps were based on the conserved
sequence segments between the two genomes. With a match
to human genome sequences, the approximate location of a
query sequence can be predicted in cattle, pig, mouse and rat
genomes based on the position of the match relatively to the
orthologous markers or the conserved segments.
Availability: The COMPASS-tool and databases are available
at http://titan.biotec.uiuc.edu/COMPASS/index.html